THEY'VE DONE IT!
Sky have rolled back the software to the previous version overnight (26th-27th). Everyone (so far) on the Digitalspy forum is reporting that this has fixed the issues. Thanks to El Reg for running the story - I am not sure it would have happened otherwise.
Btw it was not just modified boxes. I suspect there aren't many unmodified ones around any more but there were reports that unmodified units had the same problems.